SAXSdb — 9vcm

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1. Structure Basics

entry_id	9vcm
deposition_date	2025-06-06
last_revision	2026-06-10
title	NAD_dependent dehydrogenase
keywords	COMPLEX. NAD-DEPENDENT, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	33.99 Å
rg_electron	33.30 Å
i0	445011000.00
molecular_weight	111850.0 kDa
excluded_volume	107160 Å³
envelope_volume	190110 Å³
shell_volume	47154 Å³
envelope_diameter	110.3 Å
shell_rg	40.59 Å
envelope_rg	32.91 Å
shape_rg	33.27 Å
total_rg	33.75 Å
total_atoms	8483
n_residues	1151
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	107.0 Å
rg_real	33.88 Å
rg_real_error	0.74 Å
i0_real	4.4500e+08
i0_real_error	6.5320e+06
rg_reciprocal	33.95 Å
i0_reciprocal	445000000.0000
total_estimate	0.9039
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	41.0 Å
skewness	0.172
kurtosis	-0.572
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	54110000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.914

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	NADH-dependent dihydrogenase
formula_weight	35368.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	8999

MAPTGGVGESRYVKTLRQLEVALIGAGLIARLHLEAWLGAGAAVRVYSDDGRSRELAAEFGAKAAGSLEEALDGADAVDICTPTASHHEIALTAIAAGVGVVCEKPLAASAEEAEEIVTAAERAGVRLYAAHDVRFAAPYARLHELVASGRLGEGALGRFSFSAYHPRPWTGHASARSGGILTDQLLHGADLAHWVFGDVVRVHACYQGDIATPAPEGAVATGTAVLTHASGAISQVVSRWTATPRPPVRVAFHVSGTGGSVSYDSEWPQEVRVVDGGAGNFAYGGPSVFDTEMREFATAFAGGPEPRIGAKDALAAVRIIHAAAESAWTGRAVELPVRGAA

Source

organism	Amycolatopsis mediterranei S699
ncbi_taxonomy_id	713604
host_organism	Escherichia coli

Entity 2 polymer

description	RifT
formula_weight	26214.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MVKVAILSSTPQAYAGALRGLPDVEVVAAASWDAFEPVRQAAEAGARVLCEYPPAAKETDLKAMIDAAGDRLTFASPACHGEAFAVVRKGIADGGIGELTTVLGSVATSVDGVLGAAAPYLLDLADAVLGGEPAQQVYAQTNIVLSGRIGESAAVLTVRYRSGQVASFDCRRHGSATGLPAVTFIGDQGSVQYDAGPQLLGGERPELGGEDLEALMLKDFLGAGDGPGPDGQAALRTFRIIQAAYESAHTGQPVDL

Source

organism	Amycolatopsis mediterranei S699
ncbi_taxonomy_id	713604
host_organism	Escherichia coli

Entity 3 non-polymer

description	;(4Z,6E,8S,9S,10R,11R,12R,13R,14R,15S,16S,17Z,22R,23S)-4,8,10,12,14,16,18,22-octamethyl-9,11,13,15,23,26,28-heptakis(oxidanyl)-2-azabicyclo[22.3.1]octacosa-1(27),4,6,17,24(28),25-hexaene-3,19,21-trione ;
formula_weight	645.8 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	nat
entity_count	1

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	516

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6. Citations (1)

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length_a	192.182 Å
length_b	81.259 Å
length_c	90.126 Å
angle_alpha	90.00 °
angle_beta	102.84 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.400 Å
resolution_low	28.990 Å
r_factor	0.1780
r_work	0.1760
r_free	0.2280

fit	/app/data/saxs_computation/vc/9vcm/9vcm.fit
pddf	/app/data/pr_computation/vc/9vcm/9vcm.pr.out
profile	/app/data/saxs_computation/vc/9vcm/9vcm.dat

NAD_dependent dehydrogenase

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)